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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.9

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-04-30, 01:55 based on data in: /data3/Data_Processing/RNAseq_Datasets/GLDS_datasets/GLDS-379/00-RawData/FastQC_Reports

        Welcome! Not sure where to start?   Watch a tutorial video   (6:06)

        General Statistics

        Showing 282/282 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        RR8_LVR_BSL_ISS-T_OLD_BI1_R1_raw
        64.1%
        47%
        54.5
        RR8_LVR_BSL_ISS-T_OLD_BI1_R2_raw
        77.4%
        48%
        54.5
        RR8_LVR_BSL_ISS-T_OLD_BI2_R1_raw
        67.4%
        44%
        61.1
        RR8_LVR_BSL_ISS-T_OLD_BI2_R2_raw
        73.8%
        44%
        61.1
        RR8_LVR_BSL_ISS-T_OLD_BI3_R1_raw
        64.5%
        49%
        63.7
        RR8_LVR_BSL_ISS-T_OLD_BI3_R2_raw
        83.5%
        49%
        63.7
        RR8_LVR_BSL_ISS-T_OLD_BI4_R1_raw
        65.9%
        44%
        63.1
        RR8_LVR_BSL_ISS-T_OLD_BI4_R2_raw
        76.5%
        44%
        63.1
        RR8_LVR_BSL_ISS-T_OLD_BI5_R1_raw
        60.7%
        47%
        56.2
        RR8_LVR_BSL_ISS-T_OLD_BI5_R2_raw
        74.5%
        48%
        56.2
        RR8_LVR_BSL_ISS-T_OLD_BI6_R1_raw
        72.7%
        43%
        62.0
        RR8_LVR_BSL_ISS-T_OLD_BI6_R2_raw
        81.0%
        44%
        62.0
        RR8_LVR_BSL_ISS-T_OLD_BI7_R1_raw
        67.8%
        45%
        63.1
        RR8_LVR_BSL_ISS-T_OLD_BI7_R2_raw
        80.8%
        45%
        63.1
        RR8_LVR_BSL_ISS-T_OLD_BI8_R1_raw
        62.0%
        50%
        82.8
        RR8_LVR_BSL_ISS-T_OLD_BI8_R2_raw
        81.8%
        50%
        82.8
        RR8_LVR_BSL_ISS-T_OLD_BI9_R1_raw
        60.6%
        45%
        60.8
        RR8_LVR_BSL_ISS-T_OLD_BI9_R2_raw
        75.4%
        46%
        60.8
        RR8_LVR_BSL_ISS-T_YNG_BI11_R1_raw
        58.3%
        49%
        62.4
        RR8_LVR_BSL_ISS-T_YNG_BI11_R2_raw
        78.0%
        49%
        62.4
        RR8_LVR_BSL_ISS-T_YNG_BI12_R1_raw
        65.5%
        46%
        57.8
        RR8_LVR_BSL_ISS-T_YNG_BI12_R2_raw
        79.7%
        46%
        57.8
        RR8_LVR_BSL_ISS-T_YNG_BI13_R1_raw
        60.5%
        47%
        61.6
        RR8_LVR_BSL_ISS-T_YNG_BI13_R2_raw
        79.3%
        48%
        61.6
        RR8_LVR_BSL_ISS-T_YNG_BI14_R1_raw
        63.8%
        49%
        70.0
        RR8_LVR_BSL_ISS-T_YNG_BI14_R2_raw
        79.0%
        49%
        70.0
        RR8_LVR_BSL_ISS-T_YNG_BI15_R1_raw
        60.0%
        44%
        58.2
        RR8_LVR_BSL_ISS-T_YNG_BI15_R2_raw
        72.6%
        45%
        58.2
        RR8_LVR_BSL_ISS-T_YNG_BI16_R1_raw
        52.8%
        47%
        57.8
        RR8_LVR_BSL_ISS-T_YNG_BI16_R2_raw
        69.3%
        48%
        57.8
        RR8_LVR_BSL_ISS-T_YNG_BI17_R1_raw
        62.6%
        50%
        66.0
        RR8_LVR_BSL_ISS-T_YNG_BI17_R2_raw
        78.4%
        50%
        66.0
        RR8_LVR_BSL_ISS-T_YNG_BI18_R1_raw
        62.3%
        48%
        65.4
        RR8_LVR_BSL_ISS-T_YNG_BI18_R2_raw
        76.0%
        48%
        65.4
        RR8_LVR_BSL_ISS-T_YNG_BI19_R1_raw
        67.0%
        44%
        69.6
        RR8_LVR_BSL_ISS-T_YNG_BI19_R2_raw
        80.8%
        44%
        69.6
        RR8_LVR_BSL_ISS-T_YNG_BI20_R1_raw
        66.4%
        45%
        64.5
        RR8_LVR_BSL_ISS-T_YNG_BI20_R2_raw
        79.0%
        46%
        64.5
        RR8_LVR_BSL_LAR_OLD_BL11_R1_raw
        67.1%
        48%
        64.8
        RR8_LVR_BSL_LAR_OLD_BL11_R2_raw
        81.6%
        48%
        64.8
        RR8_LVR_BSL_LAR_OLD_BL12_R1_raw
        66.1%
        50%
        66.7
        RR8_LVR_BSL_LAR_OLD_BL12_R2_raw
        79.8%
        50%
        66.7
        RR8_LVR_BSL_LAR_OLD_BL13_R1_raw
        63.9%
        45%
        58.1
        RR8_LVR_BSL_LAR_OLD_BL13_R2_raw
        79.3%
        46%
        58.1
        RR8_LVR_BSL_LAR_OLD_BL14_R1_raw
        68.7%
        44%
        54.6
        RR8_LVR_BSL_LAR_OLD_BL14_R2_raw
        81.2%
        44%
        54.6
        RR8_LVR_BSL_LAR_OLD_BL15_R1_raw
        57.9%
        46%
        60.9
        RR8_LVR_BSL_LAR_OLD_BL15_R2_raw
        74.5%
        46%
        60.9
        RR8_LVR_BSL_LAR_OLD_BL16_R1_raw
        69.3%
        47%
        66.1
        RR8_LVR_BSL_LAR_OLD_BL16_R2_raw
        82.0%
        47%
        66.1
        RR8_LVR_BSL_LAR_OLD_BL17_R1_raw
        69.7%
        51%
        62.4
        RR8_LVR_BSL_LAR_OLD_BL17_R2_raw
        79.4%
        51%
        62.4
        RR8_LVR_BSL_LAR_OLD_BL18_R1_raw
        68.5%
        50%
        56.8
        RR8_LVR_BSL_LAR_OLD_BL18_R2_raw
        84.5%
        50%
        56.8
        RR8_LVR_BSL_LAR_OLD_BL19_R1_raw
        60.7%
        49%
        58.1
        RR8_LVR_BSL_LAR_OLD_BL19_R2_raw
        77.7%
        50%
        58.1
        RR8_LVR_BSL_LAR_OLD_BL20_R1_raw
        71.3%
        51%
        57.0
        RR8_LVR_BSL_LAR_OLD_BL20_R2_raw
        80.6%
        52%
        57.0
        RR8_LVR_BSL_LAR_YNG_BL10_R1_raw
        63.0%
        45%
        59.2
        RR8_LVR_BSL_LAR_YNG_BL10_R2_raw
        75.7%
        46%
        59.2
        RR8_LVR_BSL_LAR_YNG_BL1_R1_raw
        73.0%
        50%
        59.6
        RR8_LVR_BSL_LAR_YNG_BL1_R2_raw
        82.9%
        51%
        59.6
        RR8_LVR_BSL_LAR_YNG_BL2_R1_raw
        69.4%
        43%
        54.0
        RR8_LVR_BSL_LAR_YNG_BL2_R2_raw
        82.8%
        43%
        54.0
        RR8_LVR_BSL_LAR_YNG_BL4_R1_raw
        77.6%
        52%
        56.7
        RR8_LVR_BSL_LAR_YNG_BL4_R2_raw
        84.4%
        52%
        56.7
        RR8_LVR_BSL_LAR_YNG_BL5_R1_raw
        71.4%
        50%
        61.3
        RR8_LVR_BSL_LAR_YNG_BL5_R2_raw
        84.9%
        50%
        61.3
        RR8_LVR_BSL_LAR_YNG_BL6_R1_raw
        73.0%
        51%
        60.9
        RR8_LVR_BSL_LAR_YNG_BL6_R2_raw
        82.2%
        52%
        60.9
        RR8_LVR_BSL_LAR_YNG_BL7_R1_raw
        78.0%
        55%
        55.2
        RR8_LVR_BSL_LAR_YNG_BL7_R2_raw
        88.3%
        54%
        55.2
        RR8_LVR_BSL_LAR_YNG_BL8_R1_raw
        69.4%
        50%
        56.5
        RR8_LVR_BSL_LAR_YNG_BL8_R2_raw
        84.7%
        50%
        56.5
        RR8_LVR_BSL_LAR_YNG_BL9_R1_raw
        80.4%
        49%
        57.9
        RR8_LVR_BSL_LAR_YNG_BL9_R2_raw
        89.0%
        48%
        57.9
        RR8_LVR_FLT_ISS-T_OLD_FI11_R1_raw
        65.3%
        46%
        60.7
        RR8_LVR_FLT_ISS-T_OLD_FI11_R2_raw
        77.7%
        47%
        60.7
        RR8_LVR_FLT_ISS-T_OLD_FI12_R1_raw
        64.4%
        46%
        54.9
        RR8_LVR_FLT_ISS-T_OLD_FI12_R2_raw
        81.3%
        46%
        54.9
        RR8_LVR_FLT_ISS-T_OLD_FI13_R1_raw
        70.5%
        43%
        61.3
        RR8_LVR_FLT_ISS-T_OLD_FI13_R2_raw
        84.2%
        43%
        61.3
        RR8_LVR_FLT_ISS-T_OLD_FI14_R1_raw
        63.9%
        47%
        65.0
        RR8_LVR_FLT_ISS-T_OLD_FI14_R2_raw
        80.5%
        48%
        65.0
        RR8_LVR_FLT_ISS-T_OLD_FI15_R1_raw
        66.5%
        47%
        62.4
        RR8_LVR_FLT_ISS-T_OLD_FI15_R2_raw
        76.1%
        47%
        62.4
        RR8_LVR_FLT_ISS-T_OLD_FI16_R1_raw
        67.5%
        46%
        66.5
        RR8_LVR_FLT_ISS-T_OLD_FI16_R2_raw
        79.1%
        46%
        66.5
        RR8_LVR_FLT_ISS-T_OLD_FI17_R1_raw
        58.9%
        47%
        59.5
        RR8_LVR_FLT_ISS-T_OLD_FI17_R2_raw
        73.5%
        47%
        59.5
        RR8_LVR_FLT_ISS-T_OLD_FI18_R1_raw
        67.0%
        46%
        66.9
        RR8_LVR_FLT_ISS-T_OLD_FI18_R2_raw
        81.1%
        46%
        66.9
        RR8_LVR_FLT_ISS-T_OLD_FI19_R1_raw
        68.6%
        44%
        56.5
        RR8_LVR_FLT_ISS-T_OLD_FI19_R2_raw
        83.3%
        44%
        56.5
        RR8_LVR_FLT_ISS-T_OLD_FI20_R1_raw
        60.0%
        50%
        62.1
        RR8_LVR_FLT_ISS-T_OLD_FI20_R2_raw
        75.1%
        50%
        62.1
        RR8_LVR_FLT_ISS-T_YNG_FI10_R1_raw
        64.9%
        46%
        53.6
        RR8_LVR_FLT_ISS-T_YNG_FI10_R2_raw
        80.2%
        47%
        53.6
        RR8_LVR_FLT_ISS-T_YNG_FI1_R1_raw
        68.4%
        45%
        63.5
        RR8_LVR_FLT_ISS-T_YNG_FI1_R2_raw
        81.8%
        46%
        63.5
        RR8_LVR_FLT_ISS-T_YNG_FI2_R1_raw
        72.2%
        45%
        52.1
        RR8_LVR_FLT_ISS-T_YNG_FI2_R2_raw
        76.2%
        46%
        52.1
        RR8_LVR_FLT_ISS-T_YNG_FI3_R1_raw
        63.7%
        45%
        57.4
        RR8_LVR_FLT_ISS-T_YNG_FI3_R2_raw
        75.9%
        46%
        57.4
        RR8_LVR_FLT_ISS-T_YNG_FI4_R1_raw
        62.0%
        48%
        60.0
        RR8_LVR_FLT_ISS-T_YNG_FI4_R2_raw
        82.3%
        49%
        60.0
        RR8_LVR_FLT_ISS-T_YNG_FI5_R1_raw
        67.8%
        43%
        60.9
        RR8_LVR_FLT_ISS-T_YNG_FI5_R2_raw
        82.9%
        44%
        60.9
        RR8_LVR_FLT_ISS-T_YNG_FI6_R1_raw
        61.0%
        48%
        62.5
        RR8_LVR_FLT_ISS-T_YNG_FI6_R2_raw
        81.4%
        49%
        62.5
        RR8_LVR_FLT_ISS-T_YNG_FI7_R1_raw
        61.1%
        49%
        64.8
        RR8_LVR_FLT_ISS-T_YNG_FI7_R2_raw
        77.7%
        49%
        64.8
        RR8_LVR_FLT_ISS-T_YNG_FI8_R1_raw
        71.1%
        43%
        63.7
        RR8_LVR_FLT_ISS-T_YNG_FI8_R2_raw
        85.6%
        44%
        63.7
        RR8_LVR_FLT_ISS-T_YNG_FI9_R1_raw
        60.6%
        49%
        58.4
        RR8_LVR_FLT_ISS-T_YNG_FI9_R2_raw
        80.6%
        49%
        58.4
        RR8_LVR_FLT_LAR_OLD_FL11_R1_raw
        67.2%
        50%
        58.5
        RR8_LVR_FLT_LAR_OLD_FL11_R2_raw
        79.9%
        50%
        58.5
        RR8_LVR_FLT_LAR_OLD_FL15_R1_raw
        68.2%
        51%
        74.0
        RR8_LVR_FLT_LAR_OLD_FL15_R2_raw
        83.7%
        51%
        74.0
        RR8_LVR_FLT_LAR_OLD_FL16_R1_raw
        72.4%
        51%
        67.0
        RR8_LVR_FLT_LAR_OLD_FL16_R2_raw
        85.5%
        51%
        67.0
        RR8_LVR_FLT_LAR_OLD_FL3_R1_raw
        73.0%
        50%
        59.7
        RR8_LVR_FLT_LAR_OLD_FL3_R2_raw
        82.5%
        51%
        59.7
        RR8_LVR_FLT_LAR_OLD_FL4_R1_raw
        72.9%
        51%
        62.2
        RR8_LVR_FLT_LAR_OLD_FL4_R2_raw
        85.2%
        51%
        62.2
        RR8_LVR_FLT_LAR_OLD_FL7_R1_raw
        68.3%
        47%
        57.9
        RR8_LVR_FLT_LAR_OLD_FL7_R2_raw
        84.0%
        48%
        57.9
        RR8_LVR_FLT_LAR_OLD_FL8_R1_raw
        68.2%
        49%
        64.0
        RR8_LVR_FLT_LAR_OLD_FL8_R2_raw
        82.2%
        48%
        64.0
        RR8_LVR_FLT_LAR_YNG_FL13_R1_raw
        65.2%
        49%
        58.7
        RR8_LVR_FLT_LAR_YNG_FL13_R2_raw
        83.0%
        49%
        58.7
        RR8_LVR_FLT_LAR_YNG_FL14_R1_raw
        61.9%
        49%
        61.5
        RR8_LVR_FLT_LAR_YNG_FL14_R2_raw
        81.5%
        49%
        61.5
        RR8_LVR_FLT_LAR_YNG_FL17_R1_raw
        77.6%
        51%
        53.3
        RR8_LVR_FLT_LAR_YNG_FL17_R2_raw
        87.3%
        51%
        53.3
        RR8_LVR_FLT_LAR_YNG_FL18_R1_raw
        73.7%
        52%
        63.1
        RR8_LVR_FLT_LAR_YNG_FL18_R2_raw
        85.3%
        52%
        63.1
        RR8_LVR_FLT_LAR_YNG_FL1_R1_raw
        67.7%
        44%
        56.0
        RR8_LVR_FLT_LAR_YNG_FL1_R2_raw
        80.4%
        45%
        56.0
        RR8_LVR_FLT_LAR_YNG_FL2_R1_raw
        67.6%
        50%
        60.4
        RR8_LVR_FLT_LAR_YNG_FL2_R2_raw
        83.5%
        50%
        60.4
        RR8_LVR_FLT_LAR_YNG_FL5_R1_raw
        74.9%
        54%
        54.6
        RR8_LVR_FLT_LAR_YNG_FL5_R2_raw
        87.3%
        53%
        54.6
        RR8_LVR_FLT_LAR_YNG_FL6_R1_raw
        76.2%
        51%
        65.9
        RR8_LVR_FLT_LAR_YNG_FL6_R2_raw
        84.6%
        51%
        65.9
        RR8_LVR_GC_ISS-T_OLD_GI11_R1_raw
        63.7%
        46%
        63.3
        RR8_LVR_GC_ISS-T_OLD_GI11_R2_raw
        75.2%
        46%
        63.3
        RR8_LVR_GC_ISS-T_OLD_GI12_R1_raw
        60.8%
        49%
        60.7
        RR8_LVR_GC_ISS-T_OLD_GI12_R2_raw
        76.6%
        49%
        60.7
        RR8_LVR_GC_ISS-T_OLD_GI13_R1_raw
        65.8%
        45%
        78.7
        RR8_LVR_GC_ISS-T_OLD_GI13_R2_raw
        80.6%
        45%
        78.7
        RR8_LVR_GC_ISS-T_OLD_GI14_R1_raw
        63.5%
        44%
        59.5
        RR8_LVR_GC_ISS-T_OLD_GI14_R2_raw
        74.4%
        45%
        59.5
        RR8_LVR_GC_ISS-T_OLD_GI15_R1_raw
        67.1%
        45%
        57.0
        RR8_LVR_GC_ISS-T_OLD_GI15_R2_raw
        81.8%
        45%
        57.0
        RR8_LVR_GC_ISS-T_OLD_GI16_R1_raw
        64.2%
        46%
        59.3
        RR8_LVR_GC_ISS-T_OLD_GI16_R2_raw
        79.9%
        46%
        59.3
        RR8_LVR_GC_ISS-T_OLD_GI17_R1_raw
        57.6%
        48%
        61.3
        RR8_LVR_GC_ISS-T_OLD_GI17_R2_raw
        72.2%
        49%
        61.3
        RR8_LVR_GC_ISS-T_OLD_GI18_R1_raw
        64.9%
        49%
        67.7
        RR8_LVR_GC_ISS-T_OLD_GI18_R2_raw
        78.8%
        49%
        67.7
        RR8_LVR_GC_ISS-T_OLD_GI19_R1_raw
        60.2%
        49%
        63.2
        RR8_LVR_GC_ISS-T_OLD_GI19_R2_raw
        80.1%
        49%
        63.2
        RR8_LVR_GC_ISS-T_OLD_GI20_R1_raw
        65.2%
        45%
        57.8
        RR8_LVR_GC_ISS-T_OLD_GI20_R2_raw
        79.3%
        46%
        57.8
        RR8_LVR_GC_ISS-T_YNG_GI10_R1_raw
        67.6%
        47%
        60.1
        RR8_LVR_GC_ISS-T_YNG_GI10_R2_raw
        80.2%
        47%
        60.1
        RR8_LVR_GC_ISS-T_YNG_GI1_R1_raw
        64.3%
        48%
        61.8
        RR8_LVR_GC_ISS-T_YNG_GI1_R2_raw
        77.5%
        48%
        61.8
        RR8_LVR_GC_ISS-T_YNG_GI2_R1_raw
        66.1%
        44%
        58.1
        RR8_LVR_GC_ISS-T_YNG_GI2_R2_raw
        77.0%
        45%
        58.1
        RR8_LVR_GC_ISS-T_YNG_GI3_R1_raw
        65.5%
        47%
        67.0
        RR8_LVR_GC_ISS-T_YNG_GI3_R2_raw
        82.2%
        47%
        67.0
        RR8_LVR_GC_ISS-T_YNG_GI4_R1_raw
        63.9%
        48%
        61.1
        RR8_LVR_GC_ISS-T_YNG_GI4_R2_raw
        77.2%
        48%
        61.1
        RR8_LVR_GC_ISS-T_YNG_GI5_R1_raw
        66.1%
        48%
        67.6
        RR8_LVR_GC_ISS-T_YNG_GI5_R2_raw
        79.3%
        48%
        67.6
        RR8_LVR_GC_ISS-T_YNG_GI6_R1_raw
        64.3%
        48%
        62.8
        RR8_LVR_GC_ISS-T_YNG_GI6_R2_raw
        80.8%
        48%
        62.8
        RR8_LVR_GC_ISS-T_YNG_GI7_R1_raw
        63.4%
        47%
        61.7
        RR8_LVR_GC_ISS-T_YNG_GI7_R2_raw
        75.7%
        48%
        61.7
        RR8_LVR_GC_ISS-T_YNG_GI8_R1_raw
        62.8%
        46%
        56.6
        RR8_LVR_GC_ISS-T_YNG_GI8_R2_raw
        81.4%
        47%
        56.6
        RR8_LVR_GC_ISS-T_YNG_GI9_R1_raw
        66.7%
        45%
        55.1
        RR8_LVR_GC_ISS-T_YNG_GI9_R2_raw
        78.2%
        46%
        55.1
        RR8_LVR_GC_LAR_OLD_GL11_R1_raw
        70.0%
        51%
        64.7
        RR8_LVR_GC_LAR_OLD_GL11_R2_raw
        81.4%
        51%
        64.7
        RR8_LVR_GC_LAR_OLD_GL12_R1_raw
        69.3%
        48%
        55.7
        RR8_LVR_GC_LAR_OLD_GL12_R2_raw
        81.3%
        48%
        55.7
        RR8_LVR_GC_LAR_OLD_GL15_R1_raw
        63.3%
        49%
        64.5
        RR8_LVR_GC_LAR_OLD_GL15_R2_raw
        81.9%
        49%
        64.5
        RR8_LVR_GC_LAR_OLD_GL3_R1_raw
        65.9%
        43%
        55.3
        RR8_LVR_GC_LAR_OLD_GL3_R2_raw
        79.7%
        44%
        55.3
        RR8_LVR_GC_LAR_OLD_GL4_R1_raw
        73.9%
        51%
        65.0
        RR8_LVR_GC_LAR_OLD_GL4_R2_raw
        83.4%
        51%
        65.0
        RR8_LVR_GC_LAR_OLD_GL7_R1_raw
        69.0%
        50%
        62.7
        RR8_LVR_GC_LAR_OLD_GL7_R2_raw
        84.0%
        51%
        62.7
        RR8_LVR_GC_LAR_OLD_GL8_R1_raw
        67.4%
        46%
        65.0
        RR8_LVR_GC_LAR_OLD_GL8_R2_raw
        80.5%
        47%
        65.0
        RR8_LVR_GC_LAR_YNG_GL13_R1_raw
        68.5%
        50%
        66.0
        RR8_LVR_GC_LAR_YNG_GL13_R2_raw
        81.4%
        50%
        66.0
        RR8_LVR_GC_LAR_YNG_GL14_R1_raw
        67.3%
        49%
        52.0
        RR8_LVR_GC_LAR_YNG_GL14_R2_raw
        80.8%
        48%
        52.0
        RR8_LVR_GC_LAR_YNG_GL17_R1_raw
        62.3%
        49%
        58.6
        RR8_LVR_GC_LAR_YNG_GL17_R2_raw
        80.9%
        50%
        58.6
        RR8_LVR_GC_LAR_YNG_GL18_R1_raw
        74.7%
        52%
        68.1
        RR8_LVR_GC_LAR_YNG_GL18_R2_raw
        86.4%
        52%
        68.1
        RR8_LVR_GC_LAR_YNG_GL1_R1_raw
        68.7%
        50%
        52.9
        RR8_LVR_GC_LAR_YNG_GL1_R2_raw
        78.2%
        51%
        52.9
        RR8_LVR_GC_LAR_YNG_GL2_R1_raw
        71.5%
        50%
        55.7
        RR8_LVR_GC_LAR_YNG_GL2_R2_raw
        83.2%
        49%
        55.7
        RR8_LVR_GC_LAR_YNG_GL5_R1_raw
        68.1%
        49%
        59.8
        RR8_LVR_GC_LAR_YNG_GL5_R2_raw
        81.8%
        49%
        59.8
        RR8_LVR_GC_LAR_YNG_GL6_R1_raw
        71.7%
        51%
        60.4
        RR8_LVR_GC_LAR_YNG_GL6_R2_raw
        85.3%
        50%
        60.4
        RR8_LVR_VIV_ISS-T_OLD_VI11_R1_raw
        61.3%
        46%
        63.3
        RR8_LVR_VIV_ISS-T_OLD_VI11_R2_raw
        75.0%
        46%
        63.3
        RR8_LVR_VIV_ISS-T_OLD_VI12_R1_raw
        67.5%
        51%
        58.5
        RR8_LVR_VIV_ISS-T_OLD_VI12_R2_raw
        79.2%
        51%
        58.5
        RR8_LVR_VIV_ISS-T_OLD_VI13_R1_raw
        60.5%
        49%
        63.9
        RR8_LVR_VIV_ISS-T_OLD_VI13_R2_raw
        78.7%
        49%
        63.9
        RR8_LVR_VIV_ISS-T_OLD_VI14_R1_raw
        55.4%
        46%
        57.2
        RR8_LVR_VIV_ISS-T_OLD_VI14_R2_raw
        68.1%
        47%
        57.2
        RR8_LVR_VIV_ISS-T_OLD_VI16_R1_raw
        65.4%
        46%
        59.8
        RR8_LVR_VIV_ISS-T_OLD_VI16_R2_raw
        81.0%
        46%
        59.8
        RR8_LVR_VIV_ISS-T_OLD_VI17_R1_raw
        66.7%
        48%
        52.1
        RR8_LVR_VIV_ISS-T_OLD_VI17_R2_raw
        84.4%
        48%
        52.1
        RR8_LVR_VIV_ISS-T_OLD_VI18_R1_raw
        60.6%
        49%
        60.3
        RR8_LVR_VIV_ISS-T_OLD_VI18_R2_raw
        76.9%
        49%
        60.3
        RR8_LVR_VIV_ISS-T_OLD_VI19_R1_raw
        59.5%
        49%
        61.4
        RR8_LVR_VIV_ISS-T_OLD_VI19_R2_raw
        79.6%
        49%
        61.4
        RR8_LVR_VIV_ISS-T_YNG_VI10_R1_raw
        61.8%
        48%
        62.9
        RR8_LVR_VIV_ISS-T_YNG_VI10_R2_raw
        75.7%
        48%
        62.9
        RR8_LVR_VIV_ISS-T_YNG_VI1_R1_raw
        60.1%
        49%
        59.9
        RR8_LVR_VIV_ISS-T_YNG_VI1_R2_raw
        76.6%
        50%
        59.9
        RR8_LVR_VIV_ISS-T_YNG_VI2_R1_raw
        67.2%
        44%
        54.9
        RR8_LVR_VIV_ISS-T_YNG_VI2_R2_raw
        82.9%
        45%
        54.9
        RR8_LVR_VIV_ISS-T_YNG_VI3_R1_raw
        62.9%
        49%
        61.9
        RR8_LVR_VIV_ISS-T_YNG_VI3_R2_raw
        76.3%
        49%
        61.9
        RR8_LVR_VIV_ISS-T_YNG_VI4_R1_raw
        56.7%
        50%
        59.5
        RR8_LVR_VIV_ISS-T_YNG_VI4_R2_raw
        71.1%
        51%
        59.5
        RR8_LVR_VIV_ISS-T_YNG_VI5_R1_raw
        61.5%
        49%
        60.9
        RR8_LVR_VIV_ISS-T_YNG_VI5_R2_raw
        79.5%
        49%
        60.9
        RR8_LVR_VIV_ISS-T_YNG_VI6_R1_raw
        60.1%
        50%
        49.3
        RR8_LVR_VIV_ISS-T_YNG_VI6_R2_raw
        74.8%
        50%
        49.3
        RR8_LVR_VIV_ISS-T_YNG_VI7_R1_raw
        64.3%
        49%
        57.3
        RR8_LVR_VIV_ISS-T_YNG_VI7_R2_raw
        80.5%
        49%
        57.3
        RR8_LVR_VIV_ISS-T_YNG_VI8_R1_raw
        59.8%
        49%
        59.1
        RR8_LVR_VIV_ISS-T_YNG_VI8_R2_raw
        78.2%
        49%
        59.1
        RR8_LVR_VIV_LAR_OLD_VL11_R1_raw
        63.1%
        46%
        56.5
        RR8_LVR_VIV_LAR_OLD_VL11_R2_raw
        77.2%
        46%
        56.5
        RR8_LVR_VIV_LAR_OLD_VL12_R1_raw
        67.4%
        49%
        66.6
        RR8_LVR_VIV_LAR_OLD_VL12_R2_raw
        81.8%
        49%
        66.6
        RR8_LVR_VIV_LAR_OLD_VL15_R1_raw
        68.1%
        44%
        59.1
        RR8_LVR_VIV_LAR_OLD_VL15_R2_raw
        80.8%
        45%
        59.1
        RR8_LVR_VIV_LAR_OLD_VL16_R1_raw
        74.7%
        51%
        56.5
        RR8_LVR_VIV_LAR_OLD_VL16_R2_raw
        83.4%
        51%
        56.5
        RR8_LVR_VIV_LAR_OLD_VL20_R1_raw
        72.4%
        43%
        66.7
        RR8_LVR_VIV_LAR_OLD_VL20_R2_raw
        83.8%
        43%
        66.7
        RR8_LVR_VIV_LAR_OLD_VL4_R1_raw
        72.9%
        49%
        61.5
        RR8_LVR_VIV_LAR_OLD_VL4_R2_raw
        85.9%
        49%
        61.5
        RR8_LVR_VIV_LAR_OLD_VL7_R1_raw
        67.3%
        50%
        58.6
        RR8_LVR_VIV_LAR_OLD_VL7_R2_raw
        81.0%
        49%
        58.6
        RR8_LVR_VIV_LAR_OLD_VL8_R1_raw
        68.5%
        49%
        61.6
        RR8_LVR_VIV_LAR_OLD_VL8_R2_raw
        82.8%
        49%
        61.6
        RR8_LVR_VIV_LAR_YNG_VL10_R1_raw
        71.0%
        48%
        63.5
        RR8_LVR_VIV_LAR_YNG_VL10_R2_raw
        82.1%
        48%
        63.5
        RR8_LVR_VIV_LAR_YNG_VL14_R1_raw
        65.9%
        45%
        65.4
        RR8_LVR_VIV_LAR_YNG_VL14_R2_raw
        80.8%
        45%
        65.4
        RR8_LVR_VIV_LAR_YNG_VL17_R1_raw
        76.9%
        50%
        62.9
        RR8_LVR_VIV_LAR_YNG_VL17_R2_raw
        86.2%
        50%
        62.9
        RR8_LVR_VIV_LAR_YNG_VL18_R1_raw
        72.9%
        50%
        56.7
        RR8_LVR_VIV_LAR_YNG_VL18_R2_raw
        85.3%
        50%
        56.7
        RR8_LVR_VIV_LAR_YNG_VL1_R1_raw
        68.0%
        49%
        63.8
        RR8_LVR_VIV_LAR_YNG_VL1_R2_raw
        83.9%
        48%
        63.8
        RR8_LVR_VIV_LAR_YNG_VL2_R1_raw
        72.6%
        52%
        62.7
        RR8_LVR_VIV_LAR_YNG_VL2_R2_raw
        83.9%
        51%
        62.7
        RR8_LVR_VIV_LAR_YNG_VL5_R1_raw
        71.0%
        52%
        60.4
        RR8_LVR_VIV_LAR_YNG_VL5_R2_raw
        83.1%
        52%
        60.4
        RR8_LVR_VIV_LAR_YNG_VL9_R1_raw
        78.4%
        48%
        67.8
        RR8_LVR_VIV_LAR_YNG_VL9_R2_raw
        89.8%
        48%
        67.8

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms
        282
        0
        0

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores
        282
        0
        0

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content
        0
        89
        193

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content
        7
        107
        168

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content
        282
        0
        0

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution
        282
        0
        0

        All samples have sequences of a single length (149bp).

        Sequence Duplication Levels
        0
        0
        282

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences
        0
        110
        172

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content
        1
        134
        147

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with Highcharts 5.0.600.250.50.751Section NameChart context menuExport PlotFastQC: Status ChecksBasic Stat…Basic StatisticsPer Base Sequence QuPer Tile Sequence QuPer Sequence QualityPer Base Sequence CoPer Sequence GC ContPer Base N ContentSequence Length DistSequence DuplicationOverrepresented SequAdapter ContentRR8_LVR_BSL_ISS-T_OLRR8_LVR_FLT_ISS-T_YNRR8_LVR_VIV_ISS-T_OLRR8_LVR_BSL_ISS-T_OLRR8_LVR_BSL_ISS-T_YNRR8_LVR_BSL_ISS-T_YNRR8_LVR_BSL_LAR_OLD_RR8_LVR_BSL_LAR_OLD_RR8_LVR_BSL_LAR_YNG_RR8_LVR_FLT_ISS-T_OLRR8_LVR_FLT_ISS-T_OLRR8_LVR_FLT_ISS-T_YNRR8_LVR_FLT_LAR_OLD_RR8_LVR_FLT_LAR_YNG_RR8_LVR_FLT_LAR_YNG_RR8_LVR_GC_ISS-T_OLDRR8_LVR_GC_ISS-T_OLDRR8_LVR_GC_ISS-T_YNGRR8_LVR_GC_LAR_OLD_GRR8_LVR_GC_LAR_OLD_GRR8_LVR_GC_LAR_YNG_GRR8_LVR_VIV_ISS-T_OLRR8_LVR_VIV_ISS-T_YNRR8_LVR_VIV_LAR_OLD_RR8_LVR_VIV_LAR_OLD_RR8_LVR_VIV_LAR_YNG_Created with MultiQC